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R4670/tests/comp_traces_Python_NEURON.py
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comp_traces_Python_NEURON.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-02-13 18:16:09
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-07-23 11:35:07
""" Compare output of pure-Python and NEURON acoustic simulations. """
import logging
import pickle
import matplotlib.pyplot as plt
from PointNICE.utils import logger, getNeuronsDict, si_format
from PointNICE.solvers import SolverUS, checkBatchLog, AStimWorker, setBatchDir
from PointNICE.plt import plotComp
# Set logging level
logger.setLevel(logging.INFO)
# Set neurons
neurons = ['RS', 'FS', 'LTS', 'RE', 'TC']
# neurons = ['LTS']
# Set stimulation parameters
a = 32e-9 # m
Adrive = 100e3 # Pa
Fdrive = 500e3 # Hz
PRF = 100. # Hz
DC = .5
tstim = 150e-3 # s
toffset = 100e-3 # s
ASTIM_CW_code = 'ASTIM_{}_CW_{:.0f}nm_{:.0f}kHz_{:.1f}kPa_{:.0f}ms_{}'
ASTIM_PW_code = 'ASTIM_{}_PW_{:.0f}nm_{:.0f}kHz_{:.1f}kPa_{:.0f}ms_PRF{:.2f}Hz_DC{:.2f}%_{}'
suffix = 'Python_vs_NEURON'
# Select output directory
batch_dir = setBatchDir()
mu_acc_factor = 0
# For each neuron
for nname in neurons:
if DC == 1:
simcode = ASTIM_CW_code.format(nname, a * 1e9, Fdrive * 1e-3, Adrive * 1e-3, tstim * 1e3,
suffix)
else:
simcode = ASTIM_PW_code.format(nname, a * 1e9, Fdrive * 1e-3, Adrive * 1e-3, tstim * 1e3,
PRF, DC * 1e2, suffix)
neuron = getNeuronsDict()[nname]()
# Initialize solver
solver = SolverUS(a, neuron, Fdrive)
log_filepath, _ = checkBatchLog(batch_dir, 'A-STIM')
# Run NEURON and Python A-STIM point-neuron simulations
logger.info('Running simulations for %s neuron', nname)
NEURONsim_file = AStimWorker(1, batch_dir, log_filepath, solver, neuron, Fdrive, Adrive,
tstim, toffset, PRF, DC, 'NEURON', 2).__call__()
effsim_file = AStimWorker(1, batch_dir, log_filepath, solver, neuron, Fdrive, Adrive,
tstim, toffset, PRF, DC, 'effective', 2).__call__()
# Compare computation times
with open(effsim_file, 'rb') as fh:
tcomp_eff = pickle.load(fh)['meta']['tcomp']
logger.info('Python simulation completed in %.1f s', tcomp_eff)
with open(NEURONsim_file, 'rb') as fh:
tcomp_NEURON = pickle.load(fh)['meta']['tcomp']
logger.info('NEURON simulation completed in %.1f ms (%.1f times faster)',
tcomp_NEURON * 1e3, tcomp_eff / tcomp_NEURON)
mu_acc_factor += tcomp_eff / tcomp_NEURON
# Plot resulting profiles
filepaths = [effsim_file, NEURONsim_file]
fig = plotComp('Qm', filepaths, labels=['Python', 'NEURON'], showfig=False)
ax = fig.gca()
ax.set_title('{} neuron - {}Hz, {}Pa'.format(nname, *si_format([Fdrive, Adrive], space=' ')))
fig.tight_layout()
# fig.savefig('{}/{}.png'.format(batch_dir, simcode))
mu_acc_factor /= len(neurons)
logger.info('average acceleration factor = %.1f', mu_acc_factor)
plt.show()
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